DNA extraction: The first step to identifying who lives and thrives in Antarctica

Four scientists planned the next three months of their lives in the most extreme landscape on Earth all to collect hundreds of samples of dirt.

Now dirt isn’t the end game here, the team from the University of Colorado Boulder will be collecting those samples from cryoconite holes— an isolated hole in the glacial ice created by a collection of dirt and microbes—in order to accurately identify all of the DNA profiles belonging to the microorganisms and bacteria within the hole. This investigation can help scientists know more about establishing productive microbe ecologies in the human body. Unlike a person, Antarctica has less going on in and around it. The reduced about of plants, people, and animals simplifies the complex issue of microbe ecology, said a microbiological community ecologist on the team, Pacifica Sommers.

In November 2016, Dorota Porazinska, Pacifica Sommers, Steve Schmidt and Jack Darcy begin their investigation on who and what lives within cryoconite holes near Lake Hoare, and Commonwealth and Canada Glaciers.

During a lecture at the University of Colorado Boulder, Porazinska and Sommers said that after they collect the cores of ice with frozen cryoconite holes in them, they will remove and melt what Porazinska called the “sediment patty.” After the patty is well mixed, the team will sample each hole and extract the DNA from the microorganisms and bacteria they find.

“What we see [through microscopy] are the cyanobacteria and then microscopic animals, like the rotifers and the tardigrades,” said Porazinska. “We are expecting to see at least these in the holes by just using the sequencing technologies, and of course, we are expecting to see much more ….”

“The soils in Antarctica do not support more than 10 species [of microscopic animals],” said Porazinska.

The team will travel down to Antarctica at the beginning of the season, before the cryoconite holes melt and microscopic life has the chance to interact with variables outside of its individual hole.

“You might expect that gas exchange [from a melted cryoconite hole] of the atmosphere might change, who’s around, how much they can do,” said Sommers.

In the west Antarctican plains, Porazinska’s team will hunker down in McMurdo Station, the team’s lab, and begin extracting the different DNA profiles within the soil patties. To ensure that the DNA does not degrade and that it remains specific to its own cryoconite hole the scientists will be following established DNA sequencing procedures, said Porazinska.

In order to eventually identify the owner of the DNA, the team first needs to have the cleanest DNA possible. The team will insert approximately 0.5 grams of soil into a small plastic tube with beads destined to burst the nuclei of the microscopic animals and separate the chromosomes of the bacteria. With DNA and other organic material splattering around the tube, the scientists must spin the mixture till the DNA separates from the sediment that once held it. The next steps include different solutions designed to clean and preserve the DNA, said Porazinska.

“It’s just like a cooking recipe,” said Porazinska.

When they return to the university the team and other scientists will synthesize and sequence the DNA profiles collected from each cryoconite hole.

Porazinska’s team will not be doing this aspect of the research in Antarctica because of the time limit they have on site and the immense cost to send all of the needed DNA primers, polymerase—an enzyme promoting nucleotide pairing, and machines necessary to identify who lives in what type of cryoconite hole.

Porazinska highlighted some of the obstacles they may come up against during the project.

“There are also issues of sequencing errors, amplification errors, which generate artificial species.”

For the researchers to locate the holes, collect the sediment, and extract and preserve the DNA while in Antarctica, the team ordered and mailed all of the equipment they will need to McMurdo Station, said Sommers.

“Think about all of the equipment that’s all over the lab [at the University of Colorado Boulder]; think about requesting every little piece of that on a line-item form. That’s what we worked on this summer,” said Sommers.

“The nice thing about this [requesting all the equipment], is that you really have to think very thoroughly about what you will be doing, and what you will be needing,” said Porazinska.

“We may be able to get a deeper sense of more different types of organisms using these methods [DNA sequencing],” said Sommers.

After extracting the DNA, the four-person team will preserve the DNA by adding a buffer to help stabilize the DNA while it freezes at -70 degrees Celsius in low-humidity freezers, said Porazinska.

By identifying all the organisms in the different cryoconite holes the scientists will establish what types of ecosystems these species and microbes thrive in. The team will experiment by observing different bacteria rich holes and seeing what organisms or microbes flourish or do not appear. These experiments will also try to explain how the order in which species arrive affects an environment.

DNA sequencing holds the key to establishing what species of microscopic animals and microbes can live in extreme environment of Antarctica, and those identifications may lead to greater impacts for humanity.